[gmx-users] diffusion constant of protein.

[Coincon Mathieu]

Hi,
I'm trying to calculate the Da of my protein with g_msd -mol ... -n
..     but it  I always get the coefficient for the water (~4e-5
cm^2/s).
I tried to make a "molecule"  index for my protein.
So first I tried
[ prot ]
1

and
[ prot ]
0

  I have 363 residues so I make an index with :
[ prot ]
1 2 3 4......362 363


But everything give me ~4e-5  cm^2/s or my protein should have a smaller
coefficient.
So what did I miss ?
What can I do?

Thanks by advance.

--
Mathieu Coincon PhD Student
Universite De Montreal/Departement de biochimie
Pavillon Roger Gaudry Local D345
(514).343.6111 #5352